In magnusdv/pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis

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• Title: Pedigree analysis in R
• Dates: July 28-30, 2021
• Where: Online, as part of ISFG Summer School 2021
• Teachers: Magnus Dehli Vigeland and Thore Egeland

Description

The study of genetic relatedness and how genetic information flows in families, is central in a variety of research fields, including medical and forensic genetics. The aim of this course is to introduce the elegant statistical foundations of relatedness, as well as several forensic applications, with a particular focus on using R for calculations and visualisations. Most lectures and exercises are based on the book Pedigree Analysis in R. A 30% discount will be available for participants (but you do not have to buy the book in order to attend the course).

Learning outcome

After completing the course the participants should have knowledge about:

• Classical concepts and methods of statistical genetics and relatedness analysis
• How to create, manipulate and plot pedigrees in R
• How to compute pedigree likelihoods and likelihood ratios in R
• How to perform kinship testing and pedigree reconstruction in R
• How to perform disaster victim identification in R

Prerequisites

• Basic knowledge of genetics and probability.
• Some previous experience with R is recommended.
• Please make sure that R (version > 4.0) is installed on your computer. We recommend running R from RStudio.

The following R command installs the pedsuite packages, which will be used throughout the course:

install.packages("pedsuite")

Schedule

The course runs from 14 to 18 (CEST) each day, with a 15 minute break in the middle. The lectures are aimed at 55 minutes, allowing for a short interval before exercises.

Day 1 — July 28 (Wednesday)

• 14:00–15:00 Lecture 1. Introductions (MDV)
• 15:00–15:45 Exercise set 1
• 15:45–16:00 Break
• 16:00–17:00 Lecture 2. Working with pedigrees in R (MDV)
• 17:00–18:00 Exercise set 2

Day 2 — July 29 (Thursday)

• 14:00–15:00 Lecture 3. Kinship testing: paternity cases and complex cases (TE)
• 15:00–15:45 Exercise set 3
• 15:45–16:00 Break
• 16:00–17:00 Lecture 4. Relatedness coefficients (MDV)
• 17:00–18:00 Exercise set 4

Day 3 — July 30 (Friday)

• 14:00–15:00 Lecture 5. Relatedness inference and pedigree reconstruction (MDV)
• 15:00–15:45 Exercise set 5
• 15:45–16:00 Break
• 16:00–17:00 Lecture 6. Disaster victim identification and other forensic applications (TE)
• 17:00–18:00 Exercise set 6

Comments and questions may be sent to magnusdv at gmail dot com.

magnusdv/pedsuite documentation built on Sept. 28, 2024, 1:21 a.m.